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Make sure you are comparing apples to apples when visibility permissions when building your reports. Marketo pulls anything the sync user can see, so your reports need to be built from the same level of visibility. You also want to make sure that records aren't being hidden from the sync user at some point during their life cycle that could lead to the record being deleted in Salesforce but not within the visibility of the sync user. Also, remember you are working with objects that have a 1-to-many relationship to People, Smart Lists that return the # of people with at least one object wont ever be equal to a report in Salesforce that returns the number of objects.